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Basic information

Entry
Database: PDB / ID: 8caz
Titleempty 30S head
Components
  • (30S ribosomal protein ...) x 2
  • (Small ribosomal subunit protein ...) x 6
  • 16S rRNA
  • Large ribosomal subunit protein bL31A
KeywordsRIBOSOME / Antibiotic
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / transcription antitermination factor activity, RNA binding / translational initiation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit ...negative regulation of cytoplasmic translational initiation / transcription antitermination factor activity, RNA binding / translational initiation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S2, bacteria/mitochondria/plastid / L28p-like / Ribosomal protein S2 signature 2. / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S13-like, H2TH / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS13 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS14
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.11 Å
AuthorsPaternoga, H. / Beckert, B. / Wilson, D.N.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
Other governmentDLR01Kl1820
iNEXT-Discovery871037European Union
Other governmentLM2018127
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural conservation of antibiotic interaction with ribosomes.
Authors: Helge Paternoga / Caillan Crowe-McAuliffe / Lars V Bock / Timm O Koller / Martino Morici / Bertrand Beckert / Alexander G Myasnikov / Helmut Grubmüller / Jiří Nováček / Daniel N Wilson /
Abstract: The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron- ...The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
4: Large ribosomal subunit protein bL31A
A: 16S rRNA
B: 30S ribosomal protein S2
C: Small ribosomal subunit protein uS3
G: 30S ribosomal protein S7
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
S: Small ribosomal subunit protein uS19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)642,92552
Polymers641,71210
Non-polymers1,21342
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 2 types, 2 molecules BG

#3: Protein 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V0
#5: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P02359

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Small ribosomal subunit protein ... , 6 types, 6 molecules CIJMNS

#4: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7V3
#6: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7X3
#7: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7R5
#8: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7S9
#9: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AG59
#10: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7U3

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Protein / RNA chain , 2 types, 2 molecules 4A

#1: Protein Large ribosomal subunit protein bL31A / 50S ribosomal protein L31


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A7M9
#2: RNA chain 16S rRNA


Mass: 499124.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 2073407

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Non-polymers , 3 types, 660 molecules

#11: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#12: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S ribosomes with antibiotic cocktail / Type: RIBOSOME / Details: 70S + Kasugamycin, Capreomycin, Retapamulin / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
225 mMMagnesium acetateMg(OAc)21
380 mMAmmonium chlorideNH4Cl1
4100 mMPotassium acetateKOAc1
51 mMDTTC4H10O2S21
60.05 % (w/v)DDMC24H46O111
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 400 nm
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0415 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179724 / Symmetry type: POINT
RefinementResolution: 2.11→164.16 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 3.894 / SU ML: 0.093 / ESU R: 0.11
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.27621 --
obs0.27621 614685 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 56.189 Å2
Refinement stepCycle: 1 / Total: 19193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.01120030
ELECTRON MICROSCOPYr_bond_other_d00.01713419
ELECTRON MICROSCOPYr_angle_refined_deg1.2221.76829005
ELECTRON MICROSCOPYr_angle_other_deg0.4951.61231358
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.3751082
ELECTRON MICROSCOPYr_dihedral_angle_2_deg7.3415119
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.534101688
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.050.23620
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0216051
ELECTRON MICROSCOPYr_gen_planes_other0.0020.023873
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.9426.3724367
ELECTRON MICROSCOPYr_mcbond_other2.9416.3724367
ELECTRON MICROSCOPYr_mcangle_it5.06111.4895436
ELECTRON MICROSCOPYr_mcangle_other5.06111.4895437
ELECTRON MICROSCOPYr_scbond_it2.8025.23915663
ELECTRON MICROSCOPYr_scbond_other2.85.25315550
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.7139.51423570
ELECTRON MICROSCOPYr_long_range_B_refined7.74854.2124794
ELECTRON MICROSCOPYr_long_range_B_other7.73354.3124685
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.649 45553 -
obs--100 %

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